开发环境：Windows2008 R2 64位+Jdk1.7+Maven3.2.3
前提条件：安装好JDK1.7到C:\Program Files\Java\jdk1.7.0_67，下载好Maven并解压缩到一个文件夹D:\apache-maven-3.2.3，然后配置两者的环境变量
详细步骤：
1、下载页面:
https://github.com/cytoscape?page=1
https://github.com/cytoscape?page=2
2、通过下载页面找到对应桌面程序源码下载地址
https://github.com/cytoscape/cytoscape-impl
https://github.com/cytoscape/cytoscape-api
https://github.com/cytoscape/cytoscape-app-developer
https://github.com/cytoscape/cytoscape-gui-distribution
https://github.com/cytoscape/cytoscape
https://github.com/cytoscape/cytoscape-parent
https://github.com/cytoscape/cytoscape-samples
https://github.com/cytoscape/cytoscape-headless-distribution
https://github.com/cytoscape/cytoscape-support
下载后的文件截图如下
3、下载上面的地址的文件到本地电脑后，将所有压缩包文件解压，并复制到C:\Cytoscape目录
4、进入子项目C:\Cytoscape\cytoscape-develop目录，新建几个文件夹如下图
5、复制C:\Cytoscape目录下对应文件夹(去除掉首尾的cytoscape-和-develop)到C:\Cytoscape\cytoscape-develop目录下
可以DOS下复制，命令如下
xcopy /s /e C:\Cytoscape\cytoscape-parent-develop\*.* C:\Cytoscape\cytoscape-develop\parent
xcopy /s /e C:\Cytoscape\cytoscape-api-develop\*.* C:\Cytoscape\cytoscape-develop\api
xcopy /s /e C:\Cytoscape\cytoscape-impl-develop\*.* C:\Cytoscape\cytoscape-develop\impl
xcopy /s /e C:\Cytoscape\cytoscape-support-develop\*.* C:\Cytoscape\cytoscape-develop\support
xcopy /s /e C:\Cytoscape\cytoscape-gui-distribution-develop\*.* C:\Cytoscape\cytoscape-develop\gui-distribution
xcopy /s /e C:\Cytoscape\cytoscape-app-developer-develop\*.* C:\Cytoscape\cytoscape-develop\app-developer
6、DOS下进入C:\Cytoscape\cytoscape-develop目录，并执行编译命令
cd C:\Cytoscape\cytoscape-api-develop
mvn -o -Dmaven.test.skip=true clean install
7、完成后在资源管理器中进入目录C:\Cytoscape\cytoscape-develop\gui-distribution\assembly\target\cytoscape，双击目录下的cytoscape.bat文件运行程序
8、启动成功后的界面如下
9、查看对应的软件版本信息界面如下
